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1.  Clinical importance and surgical decision-making regarding proximal resection margin for gastric cancer 
Because of the intramural spread of gastric cancer, a sufficient length of a resection margin has to be attained to ensure complete excision of the tumor. There has been debate on an adequate length of proximal resection margin (PRM) and its related issues. Thus, the objective of this article is to review several studies on PRM and to summarize the current evidence on the subject. Although there is some discrepancy in the recommended values for PRM between authors, a PRM of more than 2-3 cm for early gastric cancer and 5-6 cm for advanced gastric cancer is thought to be acceptable. Once the margin is confirmed to be clear, however, the length of PRM measured in postoperative pathologic examination does not affect the patient’s survival, even when it is shorter than the recommended values. Hence, the recommendations for PRM length should be applied only to intraoperative decision-making to prevent positive margins on the final pathology. Given that a negative resection margin is the ultimate goal of determining an adequate PRM, development and improvement of reliable methods to confirm a negative resection margin intraoperatively would minimize the extent of surgery and offer a better quality of life to more patients. In the same context, special attention has to be paid to patients who have advanced stage or diffuse-type gastric cancer, because they are more likely to have a positive margin. Therefore, a wider excision with intraoperative frozen section (IFS) examination of the resection margin is necessary. Despite all the attempts to avoid positive margins, there is still a certain rate of positive-margin cases. Since the negative impact of a positive margin on prognosis is mostly obvious in low N stage patients, aggressive further management, such as extensive re-operation, is required for these patients. In conclusion, every possible preoperative and intraoperative evaluation should be thoroughly carried out to identify in advance the patients with a high risk of having positive margins; these patients need careful management with a wider excision or an IFS examination to confirm a negative margin during surgery.
PMCID: PMC3671068  PMID: 23738049
Resection margin; Proximal resection margin; Negative resection margin; Positive resection margin; Gastrectomy; Gastric cancer
2.  Primary Pulmonary Plasmacytoma Presenting as Multiple Lung Nodules 
PMCID: PMC3295978  PMID: 22403510
Plasmacytoma; Multiple Pulmonary Nodules; Paraproteinemias
3.  Aging over 70 Years Is Not a Decisively Dismal Prognostic Factor in Gastric Cancer Surgery 
Journal of Gastric Cancer  2011;11(4):200-205.
Gastric cancer has a high incidence and mortality rate in Korea. Despite a growing older population and an increase in the number of older patients with gastric cancer, the older patients are not willing to undergo surgery due to their operative risks. Hence, to determine the clinical characteristics and outcomes of gastric cancer surgery for them, we investigate factors influencing the treatment decision.
Materials and Methods
Between January 1996 and December 2005, a total of 1,519 patients were classified into two groups; the younger age group between 41 and 69 years of age, and the older age group of 70 years or older. The analysis conducted included patient characteristics, accompanying disorders, related American Society of Anesthesiologists (ASA) grade, pathological characteristics and survival rate for each age group.
Significant differences were found in the ASA grade (P<0.001) and the number of accompanying disorders (P<0.001) between the two groups. The average length of hospital stay after surgery was 14.5 days in the younger age group, and 13.3 days in the older age group (P=0.065). The average survival time was 47.5 months in the younger age group, and 43.2 months in the older age group (P<0.001).
This study demonstrated that there was more number of accompanying disorders with a high surgical risk in the older age group. However, there was no significant difference between the older and younger age groups in terms of the incidence of complications, under the given disease conditions and if proper management was provided.
PMCID: PMC3273689  PMID: 22324010
Stomach neoplasms; Aged; Survival
4.  Current status of robot-assisted gastric surgery 
In an effort to minimize the limitations of laparoscopy, a robotic surgery system was introduced, but its role for gastric cancer is still unclear. The objective of this article is to assess the current status of robotic surgery for gastric cancer and to predict future prospects. Although the current study was limited by its small number of patients and retrospective nature, robot-assisted gastrectomy with lymphadenectomy for the treatment of gastric cancer is a feasible and safe procedure for experienced laparoscopic surgeons. Most studies have reported satisfactory results for postoperative short-term coutcomes, such as: postoperative oral feeding, gas out, hospital stay and complications, compared with laparoscopic surgery; the difference is a longer operation time. However, robotic surgery showed a shallow learning curve compared with the familarity of conventional open surgery; after the accumulation of several cases, robotic surgery could be expected to result in a similar operation time. Robotic-assisted gastrectomy can expand the indications of minimally invasive surgery to include advanced gastric cancer by improving the ability to perform lymphadenectomy. Moreover, ”total” robotic gastrectomy can be facilitated using a robot-sewing technique and gastric submucosal tumors near the gastroesophageal junction or pylorus can be resected safely by this novel technique. In conclusion, robot-assisted gastrectomy may offer a good alternative to conventional open or laparoscopic surgery for gastric cancer, provided that long-term oncologic outcomes can be confirmed.
PMCID: PMC3205112  PMID: 22046490
Robot surgery; Stomach; Minimally invasive surgery
5.  The Impact of Lifestyle Behaviors on the Acquisition of Pandemic (H1N1) Influenza Infection: A Case-Control Study 
Yonsei Medical Journal  2014;55(2):422-427.
The purpose of this study was to evaluate the effects of lifestyle behaviors and health habits on the risk for acquiring pandemic influenza (H1N1) virus infection.
Materials and Methods
We conducted a case-control study in a secondary care hospital in South Korea between November 2009 and August 2010. We enrolled patients with H1N1 infection, as confirmed by a positive result of the real-time reverse transcriptase polymerase chain reaction assay; for each patient, we enrolled 4 age- and gender-matched controls with no history of H1N1 infection or severe acute respiratory illness during the H1N1 pandemic in South Korea (1:4 match).
During the study period, 33 cases and 132 age- and gender-matched controls were enrolled. The case group had a higher percentage of current smokers (p<0.01), fewer subjects reporting regular physical activity (p=0.03), or regular vitamin supplementation (p<0.01), and more subjects reporting a higher annual incidence of the common cold (p=0.048) as compared to the control group. In the multivariable analysis, 2 factors were independently associated with the acquisition of H1N1 infection: current smoking [adjusted odds ratio (OR)=5.53; 95% confidence interval (CI), 1.60-19.16; p<0.01] and a higher annual incidence of the common cold (adjusted OR=1.24; 95% CI, 1.002-1.53; p=0.048).
A current smoking status and a history of frequent colds were associated with an increased risk of acquiring H1N1 infection.
PMCID: PMC3936633  PMID: 24532513
Influenza A virus; H1N1 subtype; life style; smoking
6.  The Extended Rapid Response System: 1-Year Experience in a University Hospital 
Journal of Korean Medical Science  2014;29(3):423-430.
The rapid response system (RRS) is an innovative system designed for in-hospital, at-risk patients but underutilization of the RRS generally results in unexpected cardiopulmonary arrests. We implemented an extended RRS (E-RRS) that was triggered by actively screening at-risk patients prior to calls from primary medical attendants. These patients were identified from laboratory data, emergency consults, and step-down units. A four-member rapid response team was assembled that included an ICU staff, and the team visited the patients more than twice per day for evaluation, triage, and treatment of the patients with evidence of acute physiological decline. The goal was to provide this treatment before the team received a call from the patient's primary physician. We sought to describe the effectiveness of the E-RRS at preventing sudden and unexpected arrests and in-hospital mortality. Over the 1-yr intervention period, 2,722 patients were screened by the E-RRS program from 28,661 admissions. There were a total of 1,996 E-RRS activations of simple consultations for invasive procedures. After E-RRS implementation, the mean hospital code rate decreased by 31.1% and the mean in-hospital mortality rate was reduced by 15.3%. In conclusion, the implementation of E-RRS is associated with a reduction in the in-hospital code and mortality rates.
Graphical Abstract
PMCID: PMC3945140  PMID: 24616594
Rapid Response System; Implementation; Extended RRS; At-Risk Patient; Death, Sudden, Cardiac; Mortality
7.  Surgical extraction of mandibular third molar in pterygomandibular space: a case report 
Impacted mandibular third molars are located between the second mandibular molar and mandibular ramus. However, ectopic mandibular third molars with heterotopic positions are reported in the subcondylar or pterygomandibular space. The usual cause of malposition is a cyst or tumor, and malposition without a pathology is rare. This case report described an impacted mandibular third molar in the pterygomandibular space without any associated pathology.
PMCID: PMC3858136  PMID: 24471052
Third molar; Pterygomandibular space
8.  The stromal factors SDF1α, sFRP1 and VEGFD induce dopaminergic neuron differentiation of human pluripotent stem cells 
Journal of Neuroscience Research  2012;90(7):1367-1381.
Human embryonic stem cell (hESC)-derived dopaminergic (DA) neurons hold potential for treating Parkinson’s disease (PD) through cell replacement therapy. Generation of DA neurons from hESCs has been achieved by co-culture with the stromal cell line PA6, a source of stromal cell-derived inducing activity (SDIA). However, the factor(s) produced by stromal cells that constitute SDIA are largely undefined. We previously reported that medium conditioned by PA6 cells can generate functional DA neurons from NTera2 human embryonal carcinoma stem cells. Here we show that PA6-conditioned medium can induce DA neuronal differentiation in both NTera2 cells and the hESC I6 cell line. To identify the factor(s) responsible for SDIA, we used large-scale microarray analysis of gene expression combined with mass spectrometric analysis of PA6-conditioned medium (CM). The candidate factors, hepatocyte growth factor (HGF), stromal cell-derived factor-1 α (SDF1α), secreted frizzled-related protein 1 (sFRP1), and vascular endothelial growth factor D (VEGFD) were identified and their concentrations in PA6 CM were established by immunoaffinity capillary electrophoresis. Upon addition of SDF1α, sFRP1 and VEGFD to the culture medium we observed an increase in the number of cells expressing tyrosine hydroxylase (a marker for DA neurons) and beta-III tubulin (a marker for immature neurons) in both the NTera2 and I6 cell lines. These results indicate that SDF1α, sFRP1 and VEGFD are major components of SDIA, and suggest the potential use of these defined factors to elicit DA differentiation of pluripotent human stem cells for therapeutic intervention in PD.
PMCID: PMC3350575  PMID: 22535492
dopaminergic neurons; neuronal differentiation; stromal cell derived inducing activity; embryonic stem cells
9.  Effective correction of experimental errors in quantitative proteomics using stable isotope labeling by amino acids in cell culture (SILAC) 
Journal of Proteomics  2012;75(12):3720-3732.
Accurate and reliable quantitative proteomics in cell culture has been considerably facilitated by the introduction of the stable isotope labeling by amino acids in cell culture (SILAC), combined with high resolution mass spectrometry. There are however several major sources of quantification errors that commonly occur with SILAC techniques, i.e. incomplete incorporation of isotopic amino acids, arginine-to-proline conversion, and experimental errors in final sample mixing. Dataset normalization is a widely adopted solution to such errors, however this may not completely prevent introducing incorrect expression ratios. Here we demonstrate that a label-swap replication of SILAC experiments was able to effectively correct experimental errors by averaging ratios measured in individual replicates using quantitative proteomics and phosphoproteomics of ligand treatment of neural cell cultures. Furthermore, this strategy was successfully applied to a SILAC triplet experiment, which presents a much more complicated experimental matrix, affected by both incomplete labeling and arginine-to-proline conversion. Based on our results, we suggest that SILAC experiments should be designed to incorporate label-swap replications for enhanced reliability in expression ratios.
PMCID: PMC3394155  PMID: 22575385
SILAC; incomplete isotope labeling; arginine-to-proline conversion; label-swap replication; receptor
10.  Cerebral Air Embolism Following Pigtail Catheter Insertion for Pleural Fluid Drainage 
Pigtail catheter drainage is a common procedure for the treatment of pleural effusion and pneumothorax. The most common complications of pigtail catheter insertion are pneumothorax, hemorrhage and chest pains. Cerebral air embolism is rare, but often fatal. In this paper, we report a case of cerebral air embolism in association with the insertion of a pigtail catheter for the drainage of a pleural effusion. A 67-year-old man is being presented with dyspnea, cough and right-side chest pains and was administered antibiotics for the treatment of pneumonia. The pneumonia failed to resolve and a loculated parapneumonic pleural effusion developed. A pigtail catheter was inserted in order to drain the pleural effusion, which resulted in cerebral air embolism. The patient was administered high-flow oxygen therapy and recovered without any neurologic complications.
PMCID: PMC3695312  PMID: 23814602
Embolism, Air; Chest Tubes; Pleural Effusion
11.  TIARA genome database: update 2013 
The Total Integrated Archive of short-Read and Array (TIARA; database stores and integrates human genome data generated from multiple technologies including next-generation sequencing and high-resolution comparative genomic hybridization array. The TIARA genome browser is a powerful tool for the analysis of personal genomic information by exploring genomic variants such as SNPs, indels and structural variants simultaneously. As of September 2012, the TIARA database provides raw data and variant information for 13 sequenced whole genomes, 16 sequenced transcriptomes and 33 high resolution array assays. Sequencing reads are available at a depth of ∼30× for whole genomes and 50× for transcriptomes. Information on genomic variants includes a total of ∼9.56 million SNPs, 23 025 of which are non-synonymous SNPs, and ∼1.19 million indels. In this update, by adding high coverage sequencing of additional human individuals, the TIARA genome database now provides an extensive record of rare variants in humans. Following TIARA’s fundamentally integrative approach, new transcriptome sequencing data are matched with whole-genome sequencing data in the genome browser. Users can here observe, for example, the expression levels of human genes with allele-specific quantification. Improvements to the TIARA genome browser include the intuitive display of new complex and large-scale data sets.
PMCID: PMC3602786  PMID: 23515433
12.  Clinical Effects of Gemifloxacin on the Delay of Tuberculosis Treatment 
Journal of Korean Medical Science  2013;28(3):378-382.
Although gemifloxacin has low in vitro activity against Mycobacterium tuberculosis, the effect of gemifloxacin on the delay of tuberculosis (TB) treatment has not been validated in a clinical setting. The study group included patients with culture-confirmed pulmonary TB who initially received gemifloxacin for suspected community-acquired pneumonia (CAP). Two control groups contained patients treated with other fluoroquinolones or nonfluoroquinolone antibiotics. Sixteen cases were treated with gemifloxacin for suspected CAP before TB diagnosis. Sixteen and 32 patients were treated with other fluoroquinolones and nonfluoroquinolones, respectively. The median period from the initiation of antibiotics to the administration of anti-TB medication was nine days in the gemifloxacin group, which was significantly different from the other fluoroquinolones group (35 days). The median times for the nonfluoroquinolone group and the gemifloxacin group were not significantly different. There were no significant differences between the gemifloxacin and other fluoroquinolone group in terms of symptomatic and radiographic improvements. However, the frequency of radiographic improvement in the other fluoroquinolones group tended to be higher than in the gemifloxacin group. Gemifloxacin might be the preferred fluoroquinolone for treating CAP, to alleviate any concerns about delaying TB treatment.
PMCID: PMC3594600  PMID: 23486643
Fluoroquinolones; Tuberculosis; Pneumonia
13.  Growth Inhibition by miR-519 via Multiple p21-Inducing Pathways 
Molecular and Cellular Biology  2012;32(13):2530-2548.
The microRNA miR-519 robustly inhibits cell proliferation, in turn triggering senescence and decreasing tumor growth. However, the molecular mediators of miR-519-elicited growth inhibition are unknown. Here, we systematically investigated the influence of miR-519 on gene expression profiles leading to growth cessation in HeLa human cervical carcinoma cells. By analyzing miR-519-triggered changes in protein and mRNA expression patterns and by identifying mRNAs associated with biotinylated miR-519, we uncovered two prominent subsets of miR-519-regulated mRNAs. One subset of miR-519 target mRNAs encoded DNA maintenance proteins (including DUT1, EXO1, RPA2, and POLE4); miR-519 repressed their expression and increased DNA damage, in turn raising the levels of the cyclin-dependent kinase (cdk) inhibitor p21. The other subset of miR-519 target mRNAs encoded proteins that control intracellular calcium levels (notably, ATP2C1 and ORAI1); their downregulation by miR-519 aberrantly elevated levels of cytosolic [Ca2+] storage in HeLa cells, similarly increasing p21 levels in a manner dependent on the Ca2+-activated kinases CaMKII and GSK3β. The rises in levels of DNA damage, the Ca2+ concentration, and p21 levels stimulated an autophagic phenotype in HeLa and other human carcinoma cell lines. As a consequence, ATP levels increased, and the level of activity of the AMP-activated protein kinase (AMPK) declined, further contributing to the elevation in the abundance of p21. Our results indicate that miR-519 promotes DNA damage, alters Ca2+ homeostasis, and enhances energy production; together, these processes elevate the expression level of p21, promoting growth inhibition and cell survival.
PMCID: PMC3434494  PMID: 22547681
14.  Expression of Intercellular Adhesion Molecule-1 and E-Selectin in Gastric Cancer and Their Clinical Significance 
Journal of Gastric Cancer  2012;12(3):140-148.
Among cell adhesion molecules, serum levels of intercellular adhesion molecule-1 and E-selectin are known to be correlated with the metastatic potential of gastric cancer. In the present study, the authors investigated the expression of intercellular adhesion molecule-1 and E-selectin in gastric cancer tissues and cultured gastric cancer cells, and examined their clinical value in gastric cancer.
Materials and Methods
The protein was extracted from gastric cancer tissues and cultured gastric cancer cells (MKN-28 and Kato-III) and the expression of intercellular adhesion molecule-1 and E-selectin was examined by western blotting. The clinical significance of intercellular adhesion molecule-1 and E-selectin was explored, using immunohistochemical staining of specimens from 157 gastric cancer patients.
In western blot analysis, the expressions of intercellular adhesion molecule-1 in gastric cancer tissues and cultured gastric cancer cells were increased, however, E-selectin in gastric cancer tissues and cells were not increased. Among 157 gastric cancer patients, 79 patients (50%) were intercellular adhesion molecule-1 positive and had larger tumor size, an increased depth of tumor invasion, lymph node metastasis and perineural invasion. The intercellular adhesion molecule-1 positive group showed a higher incidence of tumor recurrence (40.5%), and a poorer 3-year survival than the negative group (54.9 vs. 85.9%, respectively).
Intercellular adhesion molecule-1 is overexpressed in gastric cancer tissues and cultured gastric cancer cells, whereas E-selectin is not overexpressed. Increased expression of intercellular adhesion molecule-1 in gastric cancer could be related to the aggressive nature of the tumor, and has a poor prognostic effect on gastric cancer.
PMCID: PMC3473220  PMID: 23094225
Stomach neoplasms; Intercellular adhesion molecule-1; E-selectin
15.  Metabolic Context Regulates Distinct Hypothalamic Transcriptional Responses to Antiaging Interventions 
The hypothalamus is an essential relay in the neural circuitry underlying energy metabolism that needs to continually adapt to changes in the energetic environment. The neuroendocrine control of food intake and energy expenditure is associated with, and likely dependent upon, hypothalamic plasticity. Severe disturbances in energy metabolism, such as those that occur in obesity, are therefore likely to be associated with disruption of hypothalamic transcriptomic plasticity. In this paper, we investigated the effects of two well-characterized antiaging interventions, caloric restriction and voluntary wheel running, in two distinct physiological paradigms, that is, diabetic (db/db) and nondiabetic wild-type (C57/Bl/6) animals to investigate the contextual sensitivity of hypothalamic transcriptomic responses. We found that, both quantitatively and qualitatively, caloric restriction and physical exercise were associated with distinct transcriptional signatures that differed significantly between diabetic and non-diabetic mice. This suggests that challenges to metabolic homeostasis regulate distinct hypothalamic gene sets in diabetic and non-diabetic animals. A greater understanding of how genetic background contributes to hypothalamic response mechanisms could pave the way for the development of more nuanced therapeutics for the treatment of metabolic disorders that occur in diverse physiological backgrounds.
PMCID: PMC3427989  PMID: 22934110
16.  Correction: VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple Pharmacological Dataset Analysis 
PLoS ONE  2012;7(5):10.1371/annotation/27f1021c-b6f2-4b90-98bc-fcacd2679185.
PMCID: PMC3368955
17.  GIT2 Acts as a Potential Keystone Protein in Functional Hypothalamic Networks Associated with Age-Related Phenotypic Changes in Rats 
PLoS ONE  2012;7(5):e36975.
The aging process affects every tissue in the body and represents one of the most complicated and highly integrated inevitable physiological entities. The maintenance of good health during the aging process likely relies upon the coherent regulation of hormonal and neuronal communication between the central nervous system and the periphery. Evidence has demonstrated that the optimal regulation of energy usage in both these systems facilitates healthy aging. However, the proteomic effects of aging in regions of the brain vital for integrating energy balance and neuronal activity are not well understood. The hypothalamus is one of the main structures in the body responsible for sustaining an efficient interaction between energy balance and neurological activity. Therefore, a greater understanding of the effects of aging in the hypothalamus may reveal important aspects of overall organismal aging and may potentially reveal the most crucial protein factors supporting this vital signaling integration. In this study, we examined alterations in protein expression in the hypothalami of young, middle-aged, and old rats. Using novel combinatorial bioinformatics analyses, we were able to gain a better understanding of the proteomic and phenotypic changes that occur during the aging process and have potentially identified the G protein-coupled receptor/cytoskeletal-associated protein GIT2 as a vital integrator and modulator of the normal aging process.
PMCID: PMC3351446  PMID: 22606319
18.  VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple Pharmacological Dataset Analysis 
PLoS ONE  2012;7(5):e36911.
As pharmacological data sets become increasingly large and complex, new visual analysis and filtering programs are needed to aid their appreciation. One of the most commonly used methods for visualizing biological data is the Venn diagram. Currently used Venn analysis software often presents multiple problems to biological scientists, in that only a limited number of simultaneous data sets can be analyzed. An improved appreciation of the connectivity between multiple, highly-complex datasets is crucial for the next generation of data analysis of genomic and proteomic data streams. We describe the development of VENNTURE, a program that facilitates visualization of up to six datasets in a user-friendly manner. This program includes versatile output features, where grouped data points can be easily exported into a spreadsheet. To demonstrate its unique experimental utility we applied VENNTURE to a highly complex parallel paradigm, i.e. comparison of multiple G protein-coupled receptor drug dose phosphoproteomic data, in multiple cellular physiological contexts. VENNTURE was able to reliably and simply dissect six complex data sets into easily identifiable groups for straightforward analysis and data output. Applied to complex pharmacological datasets, VENNTURE’s improved features and ease of analysis are much improved over currently available Venn diagram programs. VENNTURE enabled the delineation of highly complex patterns of dose-dependent G protein-coupled receptor activity and its dependence on physiological cellular contexts. This study highlights the potential for such a program in fields such as pharmacology, genomics, and bioinformatics.
PMCID: PMC3351456  PMID: 22606307
19.  Stearoyl CoA Desaturase (SCD) Facilitates Proliferation of Prostate Cancer Cells through Enhancement of Androgen Receptor Transactivation 
Molecules and Cells  2011;31(4):371-377.
Stearoyl-CoA desaturase (SCD), the rate-limiting enzyme in the biosynthesis of monounsaturated fatty acids, is highly expressed in prostate cancer although the SCD protein has been known to be rapidly turned over by proteolytic cleavage. The present data demonstrate that SCD can promote proliferation of androgen receptor (AR)-positive LNCaP prostate cancer cells and enhance dihydrotestosterone (DHT)-induced AR transcriptional activity, resulting in increased expression of prostatespecific antigen (PSA) and kallikrein-related peptidase 2 (KLK2). Interestingly, among the previously reported SCDderived peptides produced by proteolytic cleavage of SCD, a peptide spanning amino acids 130-162 of SCD (SCDCoRNR) contained the CoRNR box motif (LFLII) and enhanced AR transcriptional activity. In contrast, a mutant SCD-CoRNR in which Leu136 was replaced by Ala had no effect on AR transcriptional activity. Moreover, SCDCoRNR directly interacted with AR and inhibited RIP140 suppression of AR transactivation. Knockdown of the SCD gene by SCD microRNA suppressed AR transactivation with decreased cell proliferation, suggesting that SCD may regulate the proliferation of LNCaP cells via modulation of AR transcriptional activity. Moreover, ectopic expression of SCD in LNCaP cells facilitated LNCaP tumor formation and growth in nude mice. Together, the data indicate that SCD plays a key role in the regulation of AR transcriptional activity in prostate cancer cells.
PMCID: PMC3933960  PMID: 21331774
androgen receptor; CoRNR box; PSA; Prostate cancer; SCD
21.  Discontinuous pH gradient-mediated separation of TiO2-enriched phosphopeptides 
Analytical biochemistry  2011;409(1):81-88.
Global profiling of phosphoproteomes has proven a great challenge due to the relatively low stoichiometry of protein phosphorylation and poor ionization efficiency in mass spectrometers. Effective, physiologically-relevant, phosphoproteome research relies on the efficient phosphopeptide enrichment from complex samples. Immobilized metal affinity chromatography and titanium dioxide chromatography (TOC) can greatly assist selective phosphopeptide enrichment. However, the complexity of resultant enriched samples is often still high, suggesting that further separation of enriched phosphopeptides is required. We have developed a pH-gradient elution technique for enhanced phosphopeptide identification in conjunction with TOC. Using this process, we have demonstrated its superiority to the traditional ‘one-pot’ strategies for differential protein identification. Our technique generated a highly specific separation of phosphopeptides by an applied pH-gradient between 9.2 and 11.3. The most efficient elution range for high-resolution phosphopeptide separation was between pH 9.2 and 9.4. High-resolution separation of multiply-phosphorylated peptides was primarily achieved using elution ranges > pH 9.4. Investigation of phosphopeptide sequences identified in each pH fraction indicated that phosphopeptides with phosphorylated residues proximal to acidic residues, including glutamic acid, aspartic acid, and other phosphorylated residues, were preferentially eluted at higher pH values.
PMCID: PMC3002755  PMID: 20946866
titanium dioxide; phosphoproteomics; mass spectrometry; pH-dependent elution
22.  297 Relationship Between Exhaled Nitric Oxide and Levels of Asthma Control in Asthma Patients Treated with Inhaled Corticosteroid 
While asthma control is defined as the extent to which the various manifestations of asthma are reduced by treatment, current guidelines of asthma recommend assessment of asthma control without consideration of airway inflammation. Our aim was to investigate the relationships between fractional exhaled nitric oxide (FeNO), a reliable marker of airway inflammation, and levels of asthma controls in patients treated with inhaled corticosteroid (ICS).
We enrolled 71 adult patients with asthma, who had been treated with ICS more than 4 months. Asthma control was assessed by the physician based on the Global Initiative for Asthma guidelines, and by the patients and by using Asthma Control Test (ACT). Statistical analyses were performed to analyze the relationships between FeNO and measures of asthma control and clinical indices for asthma manifestations.
There was no significant difference in FeNO levels between 3 groups according to levels of asthma control (controlled, partly controlled and uncontrolled) determined by the physician (P = 0.81) and by the patients (P = 0.81). In addition, FeNO values were not correlated with the ACT scores (r = 0.031, P = 0.807), while FeNO showed peripheral blood eosinophil counts (P < 0.001).
These findings demonstrated that FeNO levels are not related with the measures of asthma control in patients treated with ICS. Information of airway inflammation from FeNO concentrations seems to be discrepant from levels of asthma control.
PMCID: PMC3512760
23.  Clinical Outcomes of Gastrectomy after Incomplete EMR/ESD 
Journal of Gastric Cancer  2011;11(3):162-166.
Endoscopic resection is widely accepted as standard treatment for early gastric cancer (EGC) without lymph node metastasis. The procedure is minimally invasive, safe, and convenient. However, surgery is sometimes needed after endoscopic mucosal resection/endoscopic submucosal dissection endoscopic mucosal resection (EMR)/endoscopic submucosal dissection (ESD) due to perforation, bleeding, or incomplete resection. We evaluated the role of surgery after incomplete resection.
Materials and Methods
We retrospectively studied 29 patients with gastric cancer who underwent a gastrectomy after incomplete EMR/ESD from 2006 to 2010 at Korea University Hospital.
There were 13 incomplete resection cases, seven bleeding cases, three metachronous lesion cases, three recurrence cases, two perforation cases, and one lymphatic invasion case. Among the incomplete resection cases, a positive vertical margin was found in 10, a positive lateral margin in two, and a positive vertical and lateral margin in one case. Most cases (9/13) were diagnosed as mucosal tumors by endoscopic ultrasonography, but only three cases were confirmed as mucosal tumors on final pathology. The positive residual tumor rate was two of 13. The lymph node metastasis rate was three of 13. All lymph node metastasis cases were submucosal tumors with positive lymphatic invasion and no residual tumor in the gastrectomy specimen. No cases of recurrence were observed after curative resection.
A gastrectomy is required for patients with incomplete resection following EMR/ESD due to the risk of residual tumor and lymph node metastasis.
PMCID: PMC3204469  PMID: 22076221
Stomach neoplasms; EMR/ESD; Gastrectomy
24.  Regulation of Caenorhabditis elegans vitellogenesis by DAF-2/IIS through separable transcriptional and posttranscriptional mechanisms 
BMC Physiology  2011;11:11.
Evolutionary theories of aging propose that longevity evolves as a competition between reproduction and somatic maintenance for a finite pool of resources. Reproduction is thought to shorten lifespan by depleting resources from processes promoting somatic maintenance. Maternal yolk production, vitellogenesis, represents a significant maternal cost for reproduction and is suppressed under genetic and environmental conditions that extend lifespan. However, little is known about the pathways regulating vitellogenesis in response to prolongevity cues.
In order to identify mechanisms that suppress vitellogenesis under prolongevity conditions, we studied factors regulating vitellogenesis in C. elegans nematodes. In C. elegans, vitellogenesis is depressed in the absence of insulin-like signaling (IIS). We found that the C. elegans daf-2/IIS pathway regulates vitellogenesis through two mechanisms. vit-2 transcript levels in daf-2 mutants were indirectly regulated through a germline-dependent signal, and could be rescued by introduction of daf-2(+) sperm. However, yolk protein (YP) levels in daf-2 mutants were also regulated by germline-independent posttranscriptional mechanisms.
C. elegans vitellogenesis is regulated transcriptionally and posttranscriptionally in response to environmental and reproductive cues. The daf-2 pathway suppressed vitellogenesis through transcriptional mechanisms reflecting reproductive phenotypes, as well as distinct posttranscriptional mechanisms. This study reveals that pleiotropic effects of IIS pathway mutations can converge on a common downstream target, vitellogenesis, as a mechanism to modulate longevity.
PMCID: PMC3160409  PMID: 21749693
25.  Cortical gene transcription response patterns to water maze training in aged mice 
BMC Neuroscience  2011;12:63.
The hippocampus mediates the acquisition of spatial memory, but the memory trace is eventually transferred to the cortex. We have investigated transcriptional activation of pathways related to cognitive function in the cortex of the aged mouse by analyzing gene expression following water maze training.
We identified genes that were differentially responsive in aged mice with accurate spatial performance during probe trials or repeated swimming sessions, relative to home cage conditions. Effective learners exhibited significantly greater activation of several pathways, such as the mitogen-activated protein kinase and insulin receptor signaling pathways, relative to swimmers. The genes encoding activity-related cytoskeletal protein (Arc) and brain-derived neurotrophic factor (BDNF) were upregulated in proficient learners, relative to swimmers and home cage controls, while the gene encoding Rho GTPase activating protein 32 (GRIT) was downregulated. We explored the regulation of Arc, BDNF, and GRIT expression in greater morphological detail using in situ hybridization. Recall during probe trials enhanced Arc expression across multiple cortical regions involved in the cognitive component of water maze learning, while BDNF expression was more homogeneously upregulated across cortical regions involved in the associational and sensorimotor aspects of water maze training. In contrast, levels of GRIT expression were uniformly reduced across all cortical regions examined.
These results suggest that cortical gene transcription is responsive to learning in aged mice that exhibit behavioral proficiency, and support a distributed hypothesis of memory storage across multiple cortical compartments.
PMCID: PMC3142531  PMID: 21714909

Results 1-25 (46)